Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2glza1 CC-HHHHHHHHHCCCCHHHHHHHHHHHHHHHCC-CCCCCCCEEEEECC---CCCCHHHHHHHCCCCCCCCCEEECCCCC-CCEEEECCCCEEEEEEECHHHHHHHHHCC----CCC---------CCHHHHHHHHHHHHCCHHHHEEEEEEECCCCC---- >P1;d2gvia1 CCCCCCCHHHHHCCCCCC--CCHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCCCCCCEEECCCCCCEEEEECCC-CCCEEEEECCCC-CHHHHHCHHHHHHHHHCCCHHHCCHHHHHHHHHHHHHCCHHHHEEC-CCCCCCCCCCCC PSA >P1;d2glza1 67-53550255086311200001100410553b-a4469031002020---7230020012018046b78003254486-2010023b293012030289028406707----b69---------a6b43540182038194950072454856183---- >P1;d2gvia1 681501501a71733002--101100520111c1a40956501000027a56630232011001048b2600522464540000034c-550030213a81-8517950570363386857086056a00350060027183750054-538b1834a97b Translating the sequences CC-HHHHHHHHHCCCCHH**HHHHHHHHHHHCC-CCCCCCCEEEEECC---CC**HHHHHHH*CCCCCCCCEEECCCCC-**EEEECC*CEEEEEEECHHH*HHHHH*C----***---------C*HHHHHHHHHHHHCCHHHHEEE*EEECCCCC---- CC*****HHHHHCCCC**--**HHHHHHH**CC*CCCCCCC*EEEECC***CCHHHHHHHHHHCCCCCCCCEEECCCCC*EEEEE*CC-C**EEEEEC***-*HHHHHC****HHH*********CHHHHHHHHHHHHHCCHHHHEE*-***CCCCC**** 143555.tem _________________________________ CC-HHHHHHHHHCCCCHH--HHHHHHHHHHHCC-CCCCCCCEEEEECC---CCHHHHHHHHHHCCCCCCCCEEECCCCC-EEEEEECC-CEEEEEEECHHH-HHHHHHC----HHH---------CHHHHHHHHHHHHHCCHHHHEEE-EEECCCCC---- Structural block scores 0 1 C 5.0 H 6.5 7.0 3 11 H 4.1 M 3.3 3.4 12 15 C 5.0 H 4.5 3.2 16 17 H 3.0 P 1.5 1.0 18 19 - 3.0 P 0.0 75.0 20 30 H 4.3 M 1.5 1.1 31 32 C 5.0 H 7.2 6.8 34 40 C 5.0 H 5.2 5.6 41 45 E 4.6 H 0.6 0.2 46 47 C 5.0 H 1.0 1.0 48 50 - 3.0 P 75.0 7.5 51 52 C 5.0 H 4.5 6.0 53 62 H 4.4 M 0.9 1.2 63 70 C 5.0 H 5.6 4.1 71 73 E 5.0 H 1.7 2.3 74 78 C 5.0 H 5.4 4.2 80 85 E 4.0 M 0.8 0.5 86 87 C 5.0 H 7.2 8.2 90 96 E 4.4 M 1.3 1.6 98 100 H 3.0 P 5.7 6.5 102 107 H 4.3 M 4.2 5.8 109 112 - 3.0 P 75.0 3.8 113 115 H 3.0 P 8.8 4.0 116 124 - 3.0 P 75.0 5.3 126 138 H 4.8 H 4.3 3.0 139 140 C 5.0 H 5.0 4.5 141 144 H 5.0 H 4.5 3.8 145 147 E 4.3 M 3.0 3.0 149 151 E 3.0 P 5.7 5.3 152 156 C 5.0 H 4.6 5.5 157 160 - 3.0 P 75.0 9.5 >>>>>>